glmGamPoi
This is the development version of glmGamPoi; for the stable release version, see glmGamPoi.
Fit a Gamma-Poisson Generalized Linear Model
Bioconductor version: Development (3.24)
Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments.
Author: Constantin Ahlmann-Eltze [aut, cre]
, Nathan Lubock [ctb]
, Michael Love [ctb]
Maintainer: Constantin Ahlmann-Eltze <artjom31415 at googlemail.com>
citation("glmGamPoi")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("glmGamPoi")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("glmGamPoi")| glmGamPoi Quickstart | HTML | R Script |
| Pseudobulk and differential expression | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | RNASeq, Regression, SingleCell, Software |
| Version | 1.25.1 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1.0) |
| Imports | Rcpp, beachmat, DelayedMatrixStats, matrixStats, MatrixGenerics, SparseArray(>= 1.5.21), S4Vectors, DelayedArray, HDF5Array, Matrix, SummarizedExperiment, SingleCellExperiment, BiocGenerics, methods, stats, utils, splines, rlang, vctrs |
| System Requirements | C++17 |
| URL | https://github.com/const-ae/glmGamPoi |
| Bug Reports | https://github.com/const-ae/glmGamPoi/issues |
See More
| Suggests | testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, dplyr |
| Linking To | Rcpp, RcppArmadillo, beachmat, assorthead |
| Enhances | |
| Depends On Me | |
| Imports Me | BASiCStan, lemur, transformGamPoi |
| Suggests Me | DESeq2, DEXSeq, scTypeEval, singIST, scregclust, Seurat |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | glmGamPoi_1.25.1.tar.gz |
| Windows Binary (x86_64) | glmGamPoi_1.25.1.zip |
| macOS Binary (big-sur-x86_64) | glmGamPoi_1.25.1.tgz |
| macOS Binary (sonoma-arm64) | glmGamPoi_1.25.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/glmGamPoi |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/glmGamPoi |
| Bioc Package Browser | https://code.bioconductor.org/browse/glmGamPoi/ |
| Package Short Url | https://bioconductor.org/packages/glmGamPoi/ |
| Package Downloads Report | Download Stats |